DNA Sequence Duplication in
            <i>Rhodobacter sphaeroides</i>
            2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

Choudhary, Madhusudan; Fu, Yun Xin; MacKenzie, Cameron A.; Kaplan, Samuel

doi:10.1128/jb.186.7.2019-2027.2004

Cited by 19 publications

(17 citation statements)

References 44 publications

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“…Preliminary analysis of the genome of R. sphaeroides 2.4.1 facilitated our understanding of its genome organization (19). DNA duplication analysis revealed an abundance of exact DNA sequence duplications in the genome of R. sphaeroides 2.4.1, which further demonstrated that both CI and CII have coexisted in the R. sphaeroides genome (3), and this long association may have been established prior to the derivation of R. sphaeroides as a species. Optical mapping data (reference 41 and unpublished data) obtained from three strains, 2.4.1, ATCC 17029, and ATCC 17025, indicated that the sizes of CI of these stains were similar while the sizes of CII varied.…”

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confidence: 97%

Genome Analyses of Three Strains of Rhodobacter sphaeroides : Evidence of Rapid Evolution of Chromosome II

Choudhary¹,

Zanhua

et al. 2007

J Bacteriol

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Three strains of Rhodobacter sphaeroides of diverse origin have been under investigation in our laboratory for their genome complexities, including the presence of multiple chromosomes and the distribution of essential genes within their genomes. The genome of R. sphaeroides 2.4.1 has been completely sequenced and fully annotated, and now two additional strains (ATCC 17019 and ATCC 17025) of R. sphaeroides have been sequenced. Thus, genome comparisons have become a useful approach in determining the evolutionary relationships among different strains of R. sphaeroides. In this study, the concatenated chromosomal sequences from the three strains of R. sphaeroides were aligned, using Mauve, to examine the extent of shared DNA regions and the degree of relatedness among their chromosome-specific DNA sequences. In addition, the exact intraand interchromosomal DNA duplications were analyzed using Mummer. Genome analyses employing these two independent approaches revealed that strain ATCC 17025 diverged considerably from the other two strains, 2.4.1 and ATCC 17029, and that the two latter strains are more closely related to one another. Results further demonstrated that chromosome II (CII)-specific DNA sequences of R. sphaeroides have rapidly evolved, while CI-specific DNA sequences have remained highly conserved. Aside from the size variation of CII of R. sphaeroides, variation in sequence lengths of the CII-shared DNA regions and their high sequence divergence among strains of R. sphaeroides suggest the involvement of CII in the evolution of strain-specific genomic rearrangements, perhaps requiring strains to adapt in specialized niches.Rhodobacter sphaeroides, a purple nonsulfur phototrophic bacterium, belongs to the ␣-3 subgroup of the Proteobacteria (38). A number of strains with common morphological, physiological, and biochemical characteristics have been identified as representatives of this species (36); these strains were originally collected from Delft, Holland, and California from a variety of enrichment cultures. Together with the other ␣ subgroup of the Proteobacteria (12, 18), members of R. sphaeroides exhibit substantial metabolic versatility (6) and genomic complexity, including the existence of two chromosomes (23,31,32).Twenty-five strains of R. sphaeroides, including the three strains examined in the present study, have been previously investigated for their macro-restriction length polymorphisms by using pulsed-field gel electrophoresis. Multiple genetic markers derived from R. sphaeroides 2.4.1 were used to examine the genome complexity of the different strains of R. sphaeroides. Identification of diagnostic gene loci located on specific macro-restriction fragments belonging to either chromosome I (CI) or CII demonstrated the wide divergence between the two chromosomes among the different strains of R. sphaeroides. For example, the number of rrn operons varied from two to five among the different strains (23). The genome of R. sphaeroides 2.4.1 has been completely sequenced and "fully" annotated. ...

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confidence: 97%

Genome Analyses of Three Strains of Rhodobacter sphaeroides : Evidence of Rapid Evolution of Chromosome II

Choudhary¹,

Zanhua

et al. 2007

J Bacteriol

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“…Similar to Roseobacter, members of Rhodobacter are also metabolically versatile and exhibit genomic complexity (Nereng and Kaplan, 1999;Choudhary et al, 2004Choudhary et al, , 2007). …”

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confidence: 99%

Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

et al. 2008

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Within the bacterial class Alphaproteobacteria, the order Rhodobacterales contains the Roseobacter and Rhodobacter clades. Roseobacters are abundant and play important biogeochemical roles in marine environments. Roseobacter and Rhodobacter genomes contain a conserved gene transfer agent (GTA) gene cluster, and GTA-mediated gene transfer has been observed in these groups of bacteria. In this study, we investigated the genetic diversity of these two groups in Chesapeake Bay surface waters using a specific PCR primer set targeting the conserved Rhodobacterales GTA major capsid protein gene (g5). The g5 gene was successfully amplified from 26 Rhodobacterales isolates and the bay microbial communities using this primer set. Four g5 clone libraries were constructed from microbial assemblages representing different regions and seasons of the bay and yielded diverse sequences. In total, 12 distinct g5 clusters could be identified among 158 Chesapeake Bay clones, 11 fall within the Roseobacter clade, and one falls in the Rhodobacter clade. The vast majority of the clusters (10 out of 12) lack cultivated representatives. The composition of g5 sequences varied dramatically along the bay during the wintertime, and a distinct Roseobacter population composition between winter and summer was observed. The congruence between g5 and 16S rRNA gene phylogenies indicates that g5 may serve as a useful genetic marker to investigate diversity and abundance of Roseobacter and Rhodobacter in natural environments. The presence of the g5 gene in the natural populations of Roseobacter and Rhodobacter implies that genetic exchange through GTA transduction could be an important mechanism for maintaining the metabolic flexibility of these groups of bacteria.

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“…It has been suggested that the genes in the fla2 cluster could compensate for the loss of a gene in the fla1 cluster, which has been proposed to occur at low frequencies (19,28). Another possible explanation for the absence of pseudogenes in the second flagellar cluster is a recent duplication event (9), although a horizontal transfer origin for the flagellar genes in the fla1 cluster has also been proposed (20).…”

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confidence: 99%

“…Before the release of the genome sequence of this species, several gene duplications were reported to be present in its two chromosomes; these duplications included three rRNA operons (11), two hem genes (hemA and hemT) that encoded the same enzymatic activity but were differentially regulated (38,39), two sets of genes involved in CO 2 fixation for which different metabolic functions have been proposed (15,16,22), and several copies of genes encoding different chemotaxis-related proteins (50). The genome sequence of R. sphaeroides 2.4.1 revealed several additional duplications (9), including four functionally specialized copies of the rpoN gene which codes for the 54 factor (41) and two complete sets of flagellar genes (9).…”

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confidence: 99%

A Complete Set of Flagellar Genes Acquired by Horizontal Transfer Coexists with the Endogenous Flagellar System inRhodobacter sphaeroides

Poggio¹,

Abreu‐Goodger

Fabela³

et al. 2007

J Bacteriol

107

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Bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. Approximately 40 proteins are required for the assembly and functionality of this structure. Rhodobacter sphaeroides has two flagellar systems. One of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. In this work we found that the second flagellar system of R. sphaeroides can be expressed and produces a functional flagellum. In many bacteria with two flagellar systems, one is required for swimming, while the other allows movement in denser environments by producing a large number of flagella over the entire cell surface. In contrast, the second flagellar system of R. sphaeroides produces polar flagella that are required for swimming. Expression of the second set of flagellar genes seems to be positively regulated under anaerobic growth conditions. Phylogenic analysis suggests that the flagellar system that was initially characterized was in fact acquired by horizontal transfer from a ␥-proteobacterium, while the second flagellar system contains the native genes. Interestingly, other ␣-proteobacteria closely related to R. sphaeroides have also acquired a set of flagellar genes similar to the set found in R. sphaeroides, suggesting that a common ancestor received this gene cluster.The bacterial flagellum is a complex protein structure which consists of a long helical filament that is connected through a flexible linker known as the hook to an H ϩ -or Na ϩ -driven rotary motor (29). Rotation of the filament produces thrust that allows the cell to swim in liquid or semisolid medium (6). Bacteria perform taxis by controlling the frequency of reorientation, which is commonly regulated by a two-component signal transduction system that senses an environmental stimulus (2, 3, 7). Several reorientation mechanisms have been described for different bacteria (35). In Escherichia coli and Salmonella enterica serovar Typhimurium, in which the flagellar system has been studied more extensively, more than 40 proteins are required for flagellar synthesis and functioning (29). Expression of the flagellar genes is regulated in a hierarchical pattern which results from coordination of flagellar gene expression at the transcriptional or posttranscriptional level with one or more structural checkpoints in flagellum biogenesis (31). This tight regulation has probably evolved to avoid unnecessary synthesis of the large number of flagellar protein subunits required for this structure. The high energetic cost required for the synthesis and functioning of the flagellum is compensated for by the selective advantage conferred by motility. Accordingly, motility seems to be important in several processes, such as colonization, pathogenesis, dispersion, and competition for resources (37). When the growth medium is too dense to allow swimming, many bacteria differentiate in...

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DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

Cited by 19 publications

References 44 publications

Genome Analyses of Three Strains of Rhodobacter sphaeroides : Evidence of Rapid Evolution of Chromosome II

Genome Analyses of Three Strains of Rhodobacter sphaeroides : Evidence of Rapid Evolution of Chromosome II

Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

A Complete Set of Flagellar Genes Acquired by Horizontal Transfer Coexists with the Endogenous Flagellar System inRhodobacter sphaeroides

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