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Siderophore Producing Bacteria From Sugarcane Soil Isolation

ABSTRACT- Plant Growth Promoting Rhizobacteria (PGPR), are heterogeneous group of bacteria that can be found in the rhizosphere and in association with roots that enhance the quality of plant growth directly or indirectly. Siderophores are low molecular weight iron chelators which convert insoluble Fe3 to soluble Fe2 ions. For the isolation of siderophore producing bacteria, sugarcane rhizosphere soil was collected, and 10-5 and 10-6 dilutions were plated. VIT AKK-1 and VIT AKK-2 were checked for its PGPR activities. Siderophore isolation was carried out using modified CAS-agar plate method and quantification of catacholate and hydroxymate siderophore was performed. The sid-gene responsible for the production of siderophore were amplified using a gradient PCR.
Keywords: PGPR, Siderophore, Catacholate, Hydroxymate, PCR, sid-gene.
Plant growth promoting rhizobacteria (PGPR) in representation with a wide variety of soil bacteria when grown in association with a host plant, results in the stimulation of growth of their host. The direct promotion by the PGPR traits entails either providing the plant with a plant growth promoting substances that are been synthezied by the bacteria or by facilating the uptake of certain plant nutrients from the environment. The mechanism by which the PGPR may promote plant growth may include: (i) the ability to produce or to change the concentration of plant growth regulators like indole acetic acid.(ii) solubilisation of mineral phosphates and other nutrients. In addition to these PGPR traits, the PGPR bacterial strains must be rhizosphere competent that is should be able to survive and colonize in the rhizospheric soil.
The term siderophore was coined by Lankford[1] in 1973 and was used as a term to describe low molecular weight molecules that bind ferric iron and involved in the receptor specific iron transport into the bacteria. Siderophore was derived from a Greek term meaning “iron carrier” Ishimaru 1993)[2]. This is an appropriate term because the siderophore binds iron with an extremely high affinity. Many bacteria and fungi are capable of producing more than one type of siderophore or have more than one iron-uptake multiple siderophores (Neilands1981) [3]. Siderophores are classified on the basis of the chemical functional groups they use to chelate iron: (1) Catecholate-type (phenolate) siderophores bind Fe3 using adjacent hydroxyl groups of catechol rings. Enterobactin, also known as enterochelin, is produced by a number of bacteria including E. coli and is the classic example of a catechol-type siderophore (Fig. 1A) (O. Brien

White Campion Flower Genetic Degradation

The White Campion’s Masculinity Crisis
The Y chromosome of the White Campion (Silene latifolia) has undergone genetic degradation, losing some genes entirely from its Y chromosome.
Charlotte Gardener, Danielle Hewson, Abbie O’Connor, Francis Windram

This year, Bergero et al.(1) have shown that the White Campion (Silene latifolia) has lost genes from its Y sex chromosome entirely, and does not yet show significant dosage compensation. Plants which have two specific sexes, rather than consisting solely of hermaphrodites, are termed dioecious. Dioecy has arisen separately multiple times, with dioecious species found in 75% of all plant families(2). It would seem logical to assume that sex chromosomes in plants are just as common; however they are in fact surprisingly uncommon, being found in just 20 of the 648 families of plant(3). Even rarer is the presence of heteromorphic sex chromosomes – which differ between in sizes between the members of the chromosome pair.
The evolution of heteromorphic sex chromosomes relies in particular on a halt to recombination of the sex determining region of the sex chromosomes (3). Recombination occurs during meiosis, and contributes to reducing the effect of the accumulation of deletion errors in a population – known as Muller’s ratchet(2). When recombination is suppressed, chromosomes can differentiate to a point where some regions cannot be tenably recombined without interrupting the function of the gene. Whilst this allows for heterozygote-specific genotypes, it does also allow Muller’s ratchet to take effect once again. To counter this effect the sex determining chromosome (Y in an XY system) becomes less and less active, with more activity moving to the X chromosome in response (4). As these effects continue, the Y chromosome becomes effectively shortened in comparison to the paired X chromosome in a heterozygote. To compensate for the imbalance in activity between sex chromosomes, a theoretical mechanism called dosage compensation operates to balance the phenotypic expression of genes determines by the X chromosome so that expression is equal in both XX and XY organisms (5). A vast amount of the study of plant sex chromosomes has been carried out on the papaya (particularly in the case of sex chromosome evolution from autosomes) and on the White Campion (6).
The level of genetic degradation and diversity in S. latifolia is consistent with that of a drastic reduction in the Y chromosome size, supporting the hypothesis that there was a female biased ratio of dioecious plants. The X and Y chromosomes of S. latifolia are thought to have stopped recombining 5-10 mega-annum (Ma) ago, and between 10% – 20% of X-linked genes have little or no expression of their Y-linked alleles. Three reasons for this lack of expression were investigated by Bergero et al. (1) It is possible that the Y-linked copies of these genes were lost, or potentially are being expressed at an unnoticeable level, or it could be that the X-linked genes are present in regions that do not recombine with the Y, and thus are lost over time. Bergero et al. (1) began trying to uncover which hypothesis was true by identifying genes in S. latifolia which were fully X-linked and hemizygous in males (lacking Y genomic copies), of which there were 52. The “ugly sister” of S. latifolia, Silene vulgaris, a closely related species which lacks sex chromosomes, was employed as a comparison to test the theory that male hemizygoisty in S. latifolia arose through genes movement to a fully X-linked region. S.vulgaris was a perfect candidate for comparison asthe linkage group homologous with theS.latifoliafully sex-linked region is known. All genes that could be tested in S. vulgaris – genes that were male hemizygous in S. latifolia and had a variant that could be used for genotyping in S.vulgaris – were successfully mapped to the homologous sex-linked region in S. vulgaris. This suggests that these genes were carried on the same chromosome before the divergence of the two species, further implying that movement of genes onto the X chromosome is unlikely to have occurred in S.latifolia. Therefore, it is likely that S. latifolia’s Y chromosome lost genes instead of its X chromosome adding genes which had moved.

Bergero et al. (1) discovered that 14.5% of the Y chromosome has been lost in S. latifolia in the last 5-10 Ma and 15% of Y-linked genes were present but entirely unexpressed. This gives us the amount of the Y chromosome that has been lost but gives no estimate of the rate of gene loss. In the sex chromosomes of both plant and mammals some genetic regions, called strata, are suppressed before others. S. latifolia has two strata of differing ages, both of which have suffered from some gene loss (7). By mapping the X-Y genetic sequence Bergero et al. (1) found that 3% of the base pair sequence was different on the Y chromosome. This means that the 15% silence in the Y chromosome gene expression is caused by either gene loss or large sequence divergence after pseudogenisation – the process of forming non-coding genes in the DNA which have no proven biological use to the organism.
When mapped against the X chromosome, the younger of the two Y chromosome strata had a higher gene density than the older stratum, ergo; gene loss is higher in the older stratum, as expected. It was thought that any gene loss in S. latifolia occurred after a gene was silenced and therefore not of any use to the plant. However, there were similar proportions of silenced genes in both strata and indicating genes were not necessarily silenced before being lost from the chromosome.
The Y chromosome of S. latifolia although 40% larger than the X chromosome expresses far fewer genes, most likely due to gene loss. Bergero et al. (1) also investigated if there was any evidence of dosage compensation in S. latifolia. There have been multiple studies that have arrived at opposite conclusions about whether dosage compensation occurs in S. latifolia depending on the method used to measure dosage compensation (8, 9). Bergeroet al. (1) decided to recreate the Muyle et al. (8) findings and found no results showing that dosage compensation exists in S. latifolia. Bergero et al.(1) and concluded that measuring Y chromosome gene loss was the optimal method of measuring dosage compensation in S. latifolia. With this method, the authors found no evidence for dosage compensation in S. latifolia at the chromosome level. The authors hypothesised that gene-level compensation is still a possibility, however after testing they found no conclusive results to suggest that expression may happen at the gene-level. It is possible however, that dosage compensation occurs in the older stratum, as found in the mammalian XY chromosomal system. The evolution of mammalian XY chromosomes occurred much earlier than plant XY chromosomes, therefore recombination suppression has acted for longer on the genes, leading to larger amounts of dosage compensation.
Plant sex chromosomes evolved relatively recently in comparison to mammalian sex chromosomes and therefore much less is known about them. Bergero at al. (1) demonstrates that it is likely male hemizygoisty occurred in S. latifolia due to gene loss on the Y chromosome, rather than the addition of genes to the X chromosomes. It is still debated whether dosage compensation occurs in S.latifolia. Research has shown dosage compensation does not occur in S. latifolia at the chromosome level, but it is still possible that dosage compensation may operate at the gene-level.
Bergero, R. et al. Gene Loss from a Plant Sex Chromosome System. Curr Biol. 2015.
Ming, R. et al. Sex chromosomes in flowering plants. American Journal of Botany. 2007, 94(2), pp.141-150.
Ming, R. et al. Sex Chromosomes in Land Plants. Annual Review of Plant Biology, Vol 62. 2011, 62, pp.485-514.
Rice, W.R. Genetic Hitchhiking and the Evolution of Reduced Genetic-Activity of the Y-Sex Chromosome. Genetics. 1987, 116(1), pp.161-167.
Bergero, R. and Charlesworth, D. Preservation of the Y Transcriptome in a 10-Million-Year-Old Plant Sex Chromosome System. Current Biology. 2011, 21(17), pp.1470-1474.
Liu, Z. et al. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature. 2004, 427(6972), pp.348-52.
Bergero, R. et al. Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: Evidence from new sex-linked genes. Genetics. 2007, 175(4), pp.1945-1954.
Muyle, A. et al. Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes. Plos Biology. 2012, 10(4).
Chibalina, M.V. and Filatov, D.A. Plant Y Chromosome Degeneration Is Retarded by Haploid Purifying Selection. Current Biology. 2011, 21(17), pp.1475-1479.