Physical genome map of the unicellular cyanobacterium Synechococcus sp. strain PCC 7002

Abstract

A physical restriction map of the genome of the cyanobacterium Synechococcus sp. strain PCC 7002 was assembled from AscI, NotI, Sall, and SfiI digests of intact genomic DNA separated on a contour-clamped homogeneous electric field pulsed-field gel electrophoresis system. An average genome size of 2.7 X 106 bp was calculated from 21 Nod, 37 Salf, or 27 SfiI frgments obtained by the digestions. The genomic map was assembled by using three different strategies: linking clone analysis, pulsed-field fragment hybridization, and individual clone hybridization to singly and doubly restriction-digested large DNA fragments. The relative positions of 21 genes or operons were determined, and these data suggest that the gene order is not highly conserved between Synechococcus sp. strain PCC 7002 and Anabaena sp. strain PCC 7120.As a model system for the study of oxygenic photosynthesis, cyanobacteria have been used as successful tools to delineate the functional proteins involved in the light and dark reactions of photosynthesis. Several strains of cyanobacteria have been used in these experiments. These include Synechocystis sp. strain PCC 6803 (28, 43, 47), Anabaena sp. strain PCC 7120 (2), Anacystis nidulans (Synechococcus sp. strain PCC 7942) (18, 36), and Synechococcus sp. strain PCC 7002 (7). Unicellular cyanobacteria have been suggested as the progenitors of higher plant chloroplasts (16), and indeed, these prokaryotes possess as a primary energy source oxygenic photosynthesis which is similar to that found in chloroplasts of higher plants. Comparison of the molecular mechanisms of the photosynthetic apparatus between higher plant chloroplasts and cyanobacteria have shown a noteworthy similarity in protein composition and function (see reference 6 for a review).In recent years, genome mapping technology has improved to the point where large physical restriction maps can be assembled by using intact genomic DNA isolated in agarose (39, 40), cut with rare restriction site enzymes, and separated on pulsed-field gel electrophoresis (PFGE) systems (12). The ability to map complex genomes rapidly allows researchers to explore complicated questions concerning global regulation of metabolism such as genome rearrangement, i.e., heterocyst formation (20), the control and rate of DNA replication termination (25), and evolutionary aspects of genome organization (31).To better understand the genetic makeup of cyanobacteria, including genes and operons and the diurnal regulation of such operons, a project was started to construct a large-scale physical map of the genome of a unicellular cyanobacterium.

Physical and genetic map of the chromosome of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803

“…strain PCC 7120 has four psbA genes (55). In the (10). The same is true in the case of Synechocystis sp.…”

“…In Synechococcus sp. strain PCC 7002, operon psbD1C was located between rrnA and rrnB (10). In Synechocystis sp.…”

Physical map of the genome of Vibrio cholerae 569B and localization of genetic markers

“…(13), and Neisseria gonorrhoeae (14). The modified method of constructing linking-clone libraries described in the present report is perhaps the simplest among the existing methods and also allows isolation of a large number of linking clones from a FIG.…”

Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria The GenBank accession numbers for the sequences reported in this paper are AF180968 and AF180969 for ITS-L and ITS-S, respectively.

“…However, little is known about the organization of their rRNA operons. Limited data have been obtained from the physical or genetic maps of the unicellular strains Synechococcus PCC 6301 (Tomioka et al, 1981), Synechococcus PCC 7002 (Chen & Widger, 1993) and Synechocystis PCC 6803 (Kaneko et al, 1996). Further information is available from the sequences of the 16S rRNA-23S rRNA ITS domain in members of several cyanobacterial genera that include the unicellular Synechococcus PCC 6301 (Tomioka & Sugiura, 1984), Synechocystis PCC 6803 (Kaneko et al, 1996) and 47 strains of the genus Microcystis (Otsuka et al, 1999), the filamentous (non-heterocystous) Arthrospira PCC 7345 (Nelissen et al, 1994), Spirulina PCC 6313 (Nelissen et al, 1994) and Trichodesmium NIBB 1067 , the heterocystous Nodularia BCNOD 9427 (Hayes & Barker, 1997) and a strain of uncertain generic identity, ' Mastigocladus HTF ' strain PCC 7518 (G. Van der Auwera & A. Wilmotte, personal communication).…”