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Genes, Volume 2, Issue 4 (December 2011), Pages 661-1065

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Research

Jump to: Review

Open AccessArticle A Model of DNA Repeat-Assembled Mitotic Chromosomal Skeleton
Genes 2011, 2(4), 661-670; doi:10.3390/genes2040661
Received: 1 August 2011 / Revised: 15 September 2011 / Accepted: 21 September 2011 / Published: 26 September 2011
Cited by 4 | PDF Full-text (238 KB) | HTML Full-text | XML Full-text
Abstract
Despite intensive investigation for decades, the principle of higher-order organization of mitotic chromosomes is unclear. Here, I describe a novel model that emphasizes a critical role of interactions of homologous DNA repeats (repetitive elements; repetitive sequences) in mitotic chromosome architecture. According to the
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Despite intensive investigation for decades, the principle of higher-order organization of mitotic chromosomes is unclear. Here, I describe a novel model that emphasizes a critical role of interactions of homologous DNA repeats (repetitive elements; repetitive sequences) in mitotic chromosome architecture. According to the model, DNA repeats are assembled, via repeat interactions (pairing), into compact core structures that govern the arrangement of chromatins in mitotic chromosomes. Tandem repeat assemblies form a chromosomal axis to coordinate chromatins in the longitudinal dimension, while dispersed repeat assemblies form chromosomal nodes around the axis to organize chromatins in the halo. The chromosomal axis and nodes constitute a firm skeleton on which non-skeletal chromatins can be anchored, folded, and supercoiled. Full article
Open AccessArticle Functional Capabilities of the Earliest Peptides and the Emergence of Life
Genes 2011, 2(4), 671-688; doi:10.3390/genes2040671
Received: 11 August 2011 / Revised: 14 September 2011 / Accepted: 14 September 2011 / Published: 26 September 2011
Cited by 13 | PDF Full-text (317 KB) | HTML Full-text | XML Full-text
Abstract
Considering how biological macromolecules first evolved, probably within a marine environment, it seems likely the very earliest peptides were not encoded by nucleic acids, or at least not via the genetic code as we know it. An objective of the present work is
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Considering how biological macromolecules first evolved, probably within a marine environment, it seems likely the very earliest peptides were not encoded by nucleic acids, or at least not via the genetic code as we know it. An objective of the present work is to demonstrate that sequence-independent peptides, or peptides with variable and unreliable lengths and sequences, have the potential to perform a variety of chemically useful functions such as anion and cation binding and membrane and channel formation as well as simple types of catalysis. These functions tend to be performed with the assistance of the main chain CONH atoms rather than the more variable or limited side chain atoms of the peptides presumed to exist then. Full article
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
Open AccessArticle Proteomics Analysis of the Effects of Cyanate on Chromobacterium violaceum Metabolism
Genes 2011, 2(4), 736-747; doi:10.3390/genes2040736
Received: 15 August 2011 / Revised: 26 September 2011 / Accepted: 28 September 2011 / Published: 19 October 2011
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Abstract
Chromobacterium violaceum is a gram-negative betaproteobacterium that has been isolated from various Brazilian ecosystems. Its genome contains the cyn operon, which gives it the ability to metabolize highly toxic cyanate into ammonium and carbon dioxide. We used a proteomics approach to investigate the
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Chromobacterium violaceum is a gram-negative betaproteobacterium that has been isolated from various Brazilian ecosystems. Its genome contains the cyn operon, which gives it the ability to metabolize highly toxic cyanate into ammonium and carbon dioxide. We used a proteomics approach to investigate the effects of cyanate on the metabolism of this bacterium. The proteome of cells grown with and without cyanate was compared on 2-D gels. Differential spots were digested and identified by mass spectrometry. The bacterium was able to grow at concentrations of up to 1 mM cyanate. Eighteen spots were differentially expressed in the presence of cyanate, of which 16 were downregulated and only two were upregulated. An additional 12 spots were detected only in extracts of cells unexposed to cyanate, and one was expressed only by the exposed cells. Fourteen spots were identified, corresponding to 13 different proteins. We conclude that cyanate promotes expression of enzymes that combat oxidative stress and represses enzymes of the citric acid cycle, strongly affecting the energetic metabolism of the cell. Other proteins that were under-expressed in bacteria exposed to cyanate are involved in amino-acid metabolism or are hypothetical proteins, demonstrating that cyanate also affects expression of genes that are not part of the cyn operon. Full article
Open AccessArticle Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T
Genes 2011, 2(4), 763-787; doi:10.3390/genes2040763
Received: 7 September 2011 / Revised: 11 October 2011 / Accepted: 12 October 2011 / Published: 28 October 2011
Cited by 23 | PDF Full-text (1049 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another
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The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessArticle Identification of Genes Involved in the Glycosylation of Modified Viosamine of Flagellins in Pseudomonas syringae by Mass Spectrometry
Genes 2011, 2(4), 788-803; doi:10.3390/genes2040788
Received: 2 September 2011 / Revised: 20 October 2011 / Accepted: 21 October 2011 / Published: 28 October 2011
Cited by 10 | PDF Full-text (1476 KB) | HTML Full-text | XML Full-text
Abstract
Previously we revealed that flagellin proteins in Pseudomonas syringae pv. tabaci 6605 (Pta 6605) were glycosylated with a trisaccharide, modified viosamine (mVio)-rhamnose-rhamnose and that glycosylation was required for virulence. We further identified some glycosylation-related genes, including vioA, vioB, vioT, fgt1
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Previously we revealed that flagellin proteins in Pseudomonas syringae pv. tabaci 6605 (Pta 6605) were glycosylated with a trisaccharide, modified viosamine (mVio)-rhamnose-rhamnose and that glycosylation was required for virulence. We further identified some glycosylation-related genes, including vioA, vioB, vioT, fgt1, and fgt2. In this study, we newly identified vioR and vioM in a so-called viosamine island as biosynthetic genes for glycosylation of mVio in Pta 6605 by the mass spectrometry (MS) of flagellin glycan in the respective mutants. Furthermore, characterization of the mVio-related genes and MS analyses of flagellin glycans in other pathovars of P. syringae revealed that mVio-related genes were essential for mVio biosynthesis in flagellin glycans, and that P. syringae pv. syringae B728a, which does not possess a viosamine island, has a different structure of glycan in its flagellin protein. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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Open AccessArticle Isolation and Characterization of the Etheostoma tallapoosae (Teleostei: Percidae) CENP-A Gene
Genes 2011, 2(4), 829-840; doi:10.3390/genes2040829
Received: 16 March 2011 / Revised: 3 October 2011 / Accepted: 24 October 2011 / Published: 31 October 2011
Cited by 2 | PDF Full-text (525 KB) | HTML Full-text | XML Full-text
Abstract
Both centromeric alpha-satellite sequences as well as centromeric protein A (CENP-A) are highly variable in eukaryotes. CENP-A, a histone H3 variant, is thought to act as the epigenetic “mark” for assembly of centromeric proteins. While most of the histone fold domain (HFD) of
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Both centromeric alpha-satellite sequences as well as centromeric protein A (CENP-A) are highly variable in eukaryotes. CENP-A, a histone H3 variant, is thought to act as the epigenetic “mark” for assembly of centromeric proteins. While most of the histone fold domain (HFD) of the CENP-A is fairly well conserved, a portion of this HFD as well as the N-terminal tail show adaptive variation in both plants and animals. Such variation may establish reproductive barriers that may lead to speciation. The family Percidae contains over 200 species most of which are within the subfamily Etheostomatinae. This subfamily represents a species rich radiation of freshwater fishes in North America and these species exhibit both allopatric and sympatric distributions. In order to study the evolution of CENP-A in percid fish species, we have isolated and characterized the CENP-A gene from Etheostoma tallapoosae by PCR based gene walking. As a result of this study we have demonstrated that the Tallapoosa darter CENP-A gene HFD sequences can be isolated from genomic DNA by nested PCR in a manner that does not lead to the amplification of the highly sequence related histone H3 gene. We also demonstrated that PCR based walking can be subsequently used to isolate the rest of the CENP-A gene and adjacent gene sequences. These adjacent gene sequences provide us with a primer binding sites for PCR isolation of the CENP-A gene from other percid species of fishes. An initial comparison of three percid species shows that the N-terminal tail of the percid CENP-A gene shows adaptive evolution. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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Open AccessArticle Occurrence of Plasmids in the Aromatic Degrading Bacterioplankton of the Baltic Sea
Genes 2011, 2(4), 853-868; doi:10.3390/genes2040853
Received: 16 August 2011 / Revised: 23 September 2011 / Accepted: 20 October 2011 / Published: 4 November 2011
Cited by 8 | PDF Full-text (216 KB) | HTML Full-text | XML Full-text
Abstract
Plasmids are mobile genetic elements that provide their hosts with many beneficial traits including in some cases the ability to degrade different aromatic compounds. To fulfill the knowledge gap regarding catabolic plasmids of the Baltic Sea water, a total of 209 biodegrading bacterial
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Plasmids are mobile genetic elements that provide their hosts with many beneficial traits including in some cases the ability to degrade different aromatic compounds. To fulfill the knowledge gap regarding catabolic plasmids of the Baltic Sea water, a total of 209 biodegrading bacterial strains were isolated and screened for the presence of these mobile genetic elements. We found that both large and small plasmids are common in the cultivable Baltic Sea bacterioplankton and are particularly prevalent among bacterial genera Pseudomonas and Acinetobacter. Out of 61 plasmid-containing strains (29% of all isolates), 34 strains were found to carry large plasmids, which could be associated with the biodegradative capabilities of the host bacterial strains. Focusing on the diversity of IncP-9 plasmids, self-transmissible m-toluate (TOL) and salicylate (SAL) plasmids were detected. Sequencing the repA gene of IncP-9 carrying isolates revealed a high diversity within IncP-9 plasmid family, as well as extended the assumed bacterial host species range of the IncP-9 representatives. This study is the first insight into the genetic pool of the IncP-9 catabolic plasmids in the Baltic Sea bacterioplankton. Full article
Open AccessArticle Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms
Genes 2011, 2(4), 869-911; doi:10.3390/genes2040869
Received: 16 September 2011 / Revised: 28 October 2011 / Accepted: 28 October 2011 / Published: 8 November 2011
Cited by 12 | PDF Full-text (2098 KB) | HTML Full-text | XML Full-text
Abstract
The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using
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The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups. Full article
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
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Open AccessArticle Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions
Genes 2011, 2(4), 912-924; doi:10.3390/genes2040912
Received: 29 August 2011 / Revised: 7 October 2011 / Accepted: 25 October 2011 / Published: 9 November 2011
Cited by 3 | PDF Full-text (120 KB) | HTML Full-text | XML Full-text
Abstract
The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially
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The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show here for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, we do not find strong ubiquitous patterns governing the evolutionary behavior of specific functional classes. Instead, there are strong variations between the major groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints. Full article
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
Open AccessArticle Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales
Genes 2011, 2(4), 925-956; doi:10.3390/genes2040925
Received: 31 August 2011 / Revised: 24 October 2011 / Accepted: 26 October 2011 / Published: 18 November 2011
Cited by 10 | PDF Full-text (1212 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium
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Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium meliloti. The initial point of this report is a set of 52 trans-encoded sRNAs derived from the former studies. Sequence homology combined with structural conservation analyses were applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the order of Rhizobiales. This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns. Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales. Access to this data is provided via the RhizoGATE portal [1,2]. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
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Open AccessArticle Type Three Secretion System in Pseudomonas savastanoi Pathovars: Does Timing Matter?
Genes 2011, 2(4), 957-979; doi:10.3390/genes2040957
Received: 1 September 2011 / Revised: 3 November 2011 / Accepted: 4 November 2011 / Published: 25 November 2011
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Abstract
Pseudomonas savastanoi pv. savastanoi is the causal agent of Olive knot disease, relying on the Type Three Secretion System (TTSS) for its pathogenicity. In this regard, nothing was known about the two other pathovars belonging to this species, pv. nerii and pv. fraxini
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Pseudomonas savastanoi pv. savastanoi is the causal agent of Olive knot disease, relying on the Type Three Secretion System (TTSS) for its pathogenicity. In this regard, nothing was known about the two other pathovars belonging to this species, pv. nerii and pv. fraxini, characterized by a different host range. Here we report on the organization of the entire TTSS cluster on the three pathovars, and a phylogenetic analysis including the TTSS of those bacteria belonging to the P. syringae complex sequenced so far, highlighting the evolution of each operon (hrpC, hrpJ, hrpRS, hrpU and hrpZ). Moreover, by Real-Time PCR we analyzed the in vitro expression of four main TTSS genes, revealing different activation patterns in the three pathovars, hypothetically related to their diverse virulence behaviors. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
Open AccessArticle Plant-Bacteria Association and Symbiosis: Are There Common Genomic Traits in Alphaproteobacteria?
Genes 2011, 2(4), 1017-1032; doi:10.3390/genes2041017
Received: 29 September 2011 / Revised: 8 November 2011 / Accepted: 9 November 2011 / Published: 29 November 2011
Cited by 18 | PDF Full-text (529 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific
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Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessCommunication Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade
Genes 2011, 2(4), 1050-1065; doi:10.3390/genes2041050
Received: 23 October 2011 / Revised: 4 November 2011 / Accepted: 21 November 2011 / Published: 2 December 2011
Cited by 18 | PDF Full-text (1424 KB) | HTML Full-text | XML Full-text | Correction | Supplementary Files
Abstract
We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as
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We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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Review

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Open AccessReview RNA-Seq for Plant Pathogenic Bacteria
Genes 2011, 2(4), 689-705; doi:10.3390/genes2040689
Received: 16 September 2011 / Revised: 30 September 2011 / Accepted: 30 September 2011 / Published: 13 October 2011
Cited by 2 | PDF Full-text (265 KB) | HTML Full-text | XML Full-text
Abstract
The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but
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The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but it is still a technology under development with limitations and unknowns that need to be considered. Here, we review some new developments for RNA-Seq and highlight recent findings for host-associated bacteria. We also discuss the technical and statistical challenges in the practical application of RNA-Seq for studying bacterial transcriptomes and describe some of the currently available solutions. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
Open AccessReview Involvement of Type IV Pili in Pathogenicity of Plant Pathogenic Bacteria
Genes 2011, 2(4), 706-735; doi:10.3390/genes2040706
Received: 30 August 2011 / Revised: 8 October 2011 / Accepted: 10 October 2011 / Published: 18 October 2011
Cited by 11 | PDF Full-text (877 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Type IV pili (T4P) are hair-like appendages found on the surface of a wide range of bacteria belonging to the β-, γ-, and δ-Proteobacteria, Cyanobacteria and Firmicutes. They constitute an efficient device for a particular type of bacterial surface motility, named twitching, and
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Type IV pili (T4P) are hair-like appendages found on the surface of a wide range of bacteria belonging to the β-, γ-, and δ-Proteobacteria, Cyanobacteria and Firmicutes. They constitute an efficient device for a particular type of bacterial surface motility, named twitching, and are involved in several other bacterial activities and functions, including surface adherence, colonization, biofilm formation, genetic material uptake and virulence. Tens of genes are involved in T4P synthesis and regulation, with the majority of them being generally named pil/fim genes. Despite the multiple functionality of T4P and their well-established role in pathogenicity of animal pathogenic bacteria, relatively little attention has been given to the role of T4P in plant pathogenic bacteria. Only in recent years studies have begun to examine with more attention the relevance of these surface appendages for virulence of plant bacterial pathogens. The aim of this review is to summarize the current knowledge about T4P genetic machinery and its role in the interactions between phytopathogenic bacteria and their plant hosts. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
Open AccessReview The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint
Genes 2011, 2(4), 748-762; doi:10.3390/genes2040748
Received: 24 September 2011 / Revised: 15 October 2011 / Accepted: 19 October 2011 / Published: 28 October 2011
Cited by 10 | PDF Full-text (203 KB) | HTML Full-text | XML Full-text
Abstract
Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and our
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Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and our knowledge of function through a limited set of in-vitro biochemical studies. How these intersect through evolution is described in the first part of the review. In the second part, our understanding of a series of questions is addressed. This includes how sequences evolve within structures, how evolutionary processes enable structural transitions, how the folding process can change through evolution and what the fitness impacts of this might be. Moving beyond static structures, the evolution of protein kinetics (including normal modes) is discussed, as is the evolution of conformational ensembles and structurally disordered proteins. This ties back to a question of the role of neostructuralization and how it relates to selection on sequences for functions. The relationship between metastability, the fitness landscape, sequence divergence, and organismal effective population size is explored. Lastly, a brief discussion of modeling the evolution of sequences of ordered and disordered proteins is entertained. Full article
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
Open AccessReview Ecological and Temporal Constraints in the Evolution of Bacterial Genomes
Genes 2011, 2(4), 804-828; doi:10.3390/genes2040804
Received: 14 September 2011 / Revised: 10 October 2011 / Accepted: 24 October 2011 / Published: 31 October 2011
Cited by 7 | PDF Full-text (523 KB) | HTML Full-text | XML Full-text
Abstract
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present
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Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessReview Information Management of Genome Enabled Data Streams for Pseudomonas syringae on the Pseudomonas-Plant Interaction (PPI) Website
Genes 2011, 2(4), 841-852; doi:10.3390/genes2040841
Received: 2 September 2011 / Revised: 12 October 2011 / Accepted: 13 October 2011 / Published: 2 November 2011
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Abstract
Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include
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Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization. To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively. The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
Open AccessReview Insights into Cross-Kingdom Plant Pathogenic Bacteria
Genes 2011, 2(4), 980-997; doi:10.3390/genes2040980
Received: 30 August 2011 / Revised: 2 November 2011 / Accepted: 7 November 2011 / Published: 28 November 2011
Cited by 12 | PDF Full-text (240 KB) | HTML Full-text | XML Full-text
Abstract
Plant and human pathogens have evolved disease factors to successfully exploit their respective hosts. Phytopathogens utilize specific determinants that help to breach reinforced cell walls and manipulate plant physiology to facilitate the disease process, while human pathogens use determinants for exploiting mammalian physiology
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Plant and human pathogens have evolved disease factors to successfully exploit their respective hosts. Phytopathogens utilize specific determinants that help to breach reinforced cell walls and manipulate plant physiology to facilitate the disease process, while human pathogens use determinants for exploiting mammalian physiology and overcoming highly developed adaptive immune responses. Emerging research, however, has highlighted the ability of seemingly dedicated human pathogens to cause plant disease, and specialized plant pathogens to cause human disease. Such microbes represent interesting systems for studying the evolution of cross-kingdom pathogenicity, and the benefits and tradeoffs of exploiting multiple hosts with drastically different morphologies and physiologies. This review will explore cross-kingdom pathogenicity, where plants and humans are common hosts. We illustrate that while cross-kingdom pathogenicity appears to be maintained, the directionality of host association (plant to human, or human to plant) is difficult to determine. Cross-kingdom human pathogens, and their potential plant reservoirs, have important implications for the emergence of infectious diseases. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
Open AccessReview Antifragility and Tinkering in Biology (and in Business) Flexibility Provides an Efficient Epigenetic Way to Manage Risk
Genes 2011, 2(4), 998-1016; doi:10.3390/genes2040998
Received: 28 September 2011 / Revised: 25 October 2011 / Accepted: 16 November 2011 / Published: 29 November 2011
Cited by 8 | PDF Full-text (847 KB) | HTML Full-text | XML Full-text
Abstract
The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes
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The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles. Full article
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
Open AccessReview Modeling the Risk of Secondary Malignancies after Radiotherapy
Genes 2011, 2(4), 1033-1049; doi:10.3390/genes2041033
Received: 16 September 2011 / Revised: 1 November 2011 / Accepted: 4 November 2011 / Published: 29 November 2011
Cited by 13 | PDF Full-text (325 KB) | HTML Full-text | XML Full-text
Abstract
In developed countries, more than half of all cancer patients receive radiotherapy at some stage in the management of their disease. However, a radiation-induced secondary malignancy can be the price of success if the primary cancer is cured or at least controlled. Therefore,
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In developed countries, more than half of all cancer patients receive radiotherapy at some stage in the management of their disease. However, a radiation-induced secondary malignancy can be the price of success if the primary cancer is cured or at least controlled. Therefore, there is increasing concern regarding radiation-related second cancer risks in long-term radiotherapy survivors and a corresponding need to be able to predict cancer risks at high radiation doses. Of particular interest are second cancer risk estimates for new radiation treatment modalities such as intensity modulated radiotherapy, intensity modulated arc-therapy, proton and heavy ion radiotherapy. The long term risks from such modern radiotherapy treatment techniques have not yet been determined and are unlikely to become apparent for many years, due to the long latency time for solid tumor induction. Most information on the dose-response of radiation-induced cancer is derived from data on the A-bomb survivors who were exposed to γ-rays and neutrons. Since, for radiation protection purposes, the dose span of main interest is between zero and one Gy, the analysis of the A-bomb survivors is usually focused on this range. With increasing cure rates, estimates of cancer risk for doses larger than one Gy are becoming more important for radiotherapy patients. Therefore in this review, emphasis was placed on doses relevant for radiotherapy with respect to radiation induced solid cancer. Simple radiation protection models should be used only with extreme care for risk estimates in radiotherapy, since they are developed exclusively for low dose. When applied to scatter radiation, such models can predict only a fraction of observed second malignancies. Better semi-empirical models include the effect of dose fractionation and represent the dose-response relationships more accurately. The involved uncertainties are still huge for most of the organs and tissues. A major reason for this is that the underlying processes of the induction of carcinoma and sarcoma are not well known. Most uncertainties are related to the time patterns of cancer induction, the population specific dependencies and to the organ specific cancer induction rates. For radiotherapy treatment plan optimization these factors are irrelevant, as a treatment plan comparison is performed for a patient of specific age, sex, etc. If a treatment plan is compared relative to another one only the shape of the dose-response curve (the so called risk-equivalent dose) is of importance and errors can be minimized. Full article
(This article belongs to the Special Issue Radiation-Related Cancer 25 Years After Chernobyl)

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