Article

Complete genome sequence of Allochromatium vinosum DSM 180T

Standards in Genomic Sciences (Impact Factor: 3.17). 12/2011; 5(3):311-30. DOI: 10.4056/sigs.2335270
Source: PubMed

ABSTRACT

Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacterium belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus Allochromatium contains currently five species. All members were isolated from freshwater, brackish water or marine habitats and are predominately obligate phototrophs. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the Chromatiaceae within the purple sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp genome with its 3,302 protein-coding and 64 RNA genes was sequenced within the Joint Genome Institute Community Sequencing Program.

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    • "Interestingly, even though this species has yet to have its genome fully sequenced, it is reported to have 98.4% sequence identity with Alc. vinosum [1] and comparison of 16S rRNA sequences from Alc. vinosum and Alc. minutissimum indicates that these may in fact be the same species. "
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    ABSTRACT: This study systematically investigated the different types of LH2 produced by Allochromatium (Alc.) vinosum, a photosynthetic purple sulphur bacterium, in response to variations in growth conditions. Three different spectral forms of LH2 were isolated and purified, the B800-820, B800-840 and B800-850 LH2 types, all of which exhibit an unusual split 800 peak in their low temperature absorption spectra. However, it is likely that more forms are also present. Relatively more B800-820 and B800-840 are produced under low light conditions, while relatively more B800-850 is produced under high light conditions. Polypeptide compositions of the three different LH2 types were determined by a combination of HPLC and TOF/MS. The B800-820, B800-840 and B800-850 LH2 types all have a heterogeneous polypeptide composition , containing multiple types of both α and β polypeptides, and differ in their precise polypeptide composition. They all have a mixed carotenoid composition, containing carotenoids of the spirilloxanthin series. In all cases the most abundant carotenoid is rhodopin; however there is a shift towards carotenoids with a higher conjugation number in LH2 complexes produced under low light conditions. CD spectroscopy, together with the polypeptide analysis, demonstrates that these Alc. vinosum LH2 complexes are more closely related to the LH2 complex from Phs. molischianum than they are to the LH2 complexes from Rps. acidophila.
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    • "Organism Strain Size of genome ( Kb ) Number of ORFs GC % Accession number References Acidiphilium cryptum JF - 5 3963 3701 67 CP000697 Magnuson et al . , 2010 Acidiphilium multivorum AIU301 4215 4004 67 AP012035 Unpublished Allochromatium vinosum DSM180 3669 3366 64 CP001896 Weissgerber et al . , 2011 Bradyrhizobium sp . BTAi1 8494 7819 65 CP000494 Giraud et al . , 2007 ORS278 7457 6825 66 CU234118 Giraud et al . , 2007 S23321 7232 6898 64 AP012279 Okubo et al . , 2012 Brevundimonas subvibrioides ATCC15264 3445 3327 68 CP002102"
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    ABSTRACT: Studies on some purple photosynthetic bacteria have shown that the genes required for photosynthesis form a large cluster. This is often called a photosynthesis gene cluster (PGC) and has been described as a unique feature of purple photosynthetic bacteria. Here, photosynthesis genes were retrieved from the rapidly increasing genomic data of purple bacteria. Arrangements of these genes on the genomes were compared among 24 species and strains were selected from the wide distribution of alpha, beta, and gamma classes of purple bacteria. The presence of PGC was confirmed in the all of these, although it is divided into two or several islands in some species. Gene arrangements in several subclusters possibly forming an operon or a superoperon are well conserved while the directions and locations of these subclusters in the PGC vary according to the strains. Phylogenetic trees based on the sequences of the suspected products of the genes in the PGCs consistently place the species of the beta and gamma classes in a cluster within the branch of the alpha class, showing. that a horizontal transfer of PGC had occurred in the process of evolution. Information obtained from the increasing genome projects on bacteria is very useful for the study on evolution of photosynthesis and even for its application in metabolic engineering.
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    • "The bacteria were grown anaerobically in the light in RCV medium at a temperature of 30 °C and the DNA was isolated from 50 mg cell pellet. The genome of the bacteria was sequenced at the Joint Genome Institute (JGI) using a combination of Illumina and 454 technologies (Weissgerber et al., 2011). The DsrM protein sequence was extracted from A. vinosum having a protein ID ADC62196.1. "
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    ABSTRACT: This is an open access article which appeared in a journal published by Elsevier. This article is free for everyone to access, download and read. Any restrictions on use, including any restrictions on further reproduction and distribution, selling or licensing copies, or posting to personal, institutional or third party websites are defined by the user license specified on the article. For more information regarding Elsevier's open access licenses please visit: http://www.elsevier.com/openaccesslicenses Sulfur metabolism is one of the oldest known environmental processes. The operon involved in this process is called the dsr operon. The vital role of the operon is to maintain the environmental sulfur balance. The dsr operon of proteobacteria consists of 15 genes, viz. dsrABEFHCMKLJOPNRS. The proteins encoded by the dsr operon are essential for the transfer of sulfur globules from periplasm to cytosol and oxidation of the stored sulfur. In the present study we tried to analyze the probable molecular details of the DsrM proteins from a diverse set of microbial species using their sequence information. There are certain mutations in the sequences of the DsrM proteins from the different proteobacterial species. The effects of mutations in the sequences of DsrM proteins were predicted from the evolutionary point of view. This is so far the first report of its kind. Our study would therefore enable the researches to predict the hitherto unknown biochemistry of sulfur oxidation using the amino acid sequences of the DsrM proteins.
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