Very succinctly plant-bacteria interactions can be thought as governed at molecular level mainly by three types of proteins: plant PRRs (pathogen recognition receptors), bacterial effectors and plant resistance proteins. PRRs are proteins recognizing highly conserved structures and molecules in microorganisms named MAMP (microbial-associated molecular patterns) and mediate MAMP-triggered immunity (MTI), which is efficient against non-adapted pathogens. Pathogens have developed effector proteins to suppress MTI. In turn, plants can counteract the action of effector by the specific recognition of effectors mediated by resistance proteins which will trigger a strong defence response known as ETI (effector-triggered immunity) [1
During the past decade, small RNAs have also been found to be key players in mediating plant-pathogen interactions as well as many other biological processes. microRNAs (miRNAs) are important regulators of eukaryotic gene expression. They are transcribed from nuclear MIRNA
genes by RNA polymerase II (RNA pol II) into primary miRNAs (pri-miRNAs). The pri-miRNAs are then processed in plants by Dicer-like proteins (DCL) into precursor miRNAs (pre-miRNAs) which form a characteristic hairpin-like structure [2
]. A subsequent processing step by DCL slices the pre-miRNA to form a miRNA:miRNA* duplex (21-22 nt). The duplex is then methylated and exported from the nucleus to the cytoplasm where it is recognized by an argonaute (AGO) protein and incorporated into the RNA-induced silencing complex (RISC). Only the mature miRNA strand (usually the one having less stable 5' end pairing) is retained in the complex, while the passenger (miRNA*) strand becomes degraded [3
]. However, in some cases, miRNA* has been detected as being expressed at the same or even at higher levels than the leader strand and may have silencing activity [4
]. The RISC complex will guide complementary mRNA (targets) silencing, usually by cleavage between the 10th
nt of the paired miRNA [3
An early miRNA pathway control mechanism comes from MIRNA
gene transcription regulation by cis
-regulatory elements and trans
-acting factors. Recent works have attempted to identify key elements involved in miRNA regulation [5
]; however, little is yet known about miRNA co-regulation under different conditions and the mechanisms involved.
Most known plant miRNAs target transcription factors which play an important role in regulating plant development. There is now increasing evidence of miRNA's importance in response to biotic and abiotic stress in plants [2
]. Reprogrammed miRNA-mediated gene expression during plant immune response has not been studied in depth, but is potentially an important element for controlling pathogen invasion. It has been demonstrated that bacteria-induced miR393 mediates anti-bacterial defense of A. thaliana
against Pseudomonas syringae
pv. tomato (Pst) by targeting TIR1, an F-box family of auxin receptors and consequently repressing auxin signaling [11
]. In turn, bacteria use effector proteins to disrupt miRNA accumulation [12
]. The repertoire of known bacterial-responsive miRNAs has increased and includes several families known to regulate hormone signaling, such as miR160, miR167 and miR390 involved in auxin signaling, miR159 involved in ABA signaling and miR319 involved in jasmonic acid signaling [13
Cassava (Manihot esculenta)
is a staple crop which stores important quantities of starch in its roots. These roots constitute the main source of calories for more than half a billion people around the world, mainly in tropical regions [16
]. The starch also has important uses in industry, including bioethanol production [16
]. Cassava has remarkable tolerance to abiotic stress, it can be cultivated in low-fertility acidic soils and is highly tolerant to drought [16
]. Its production can be severely affected by cassava bacterial blight (CBB), caused by gram-negative bacteria Xanthomonas axonopodis
pv. manihotis (Xam)
. This disease is present in all regions where cassava is grown and production losses can reach up to 80% or 100% [19
]. CBB incidence, as that of many plant diseases, is expected to increase greatly with climate change [20
]. This, along with the increasing human population, makes it essential to understand the underlying mechanism of plant antibacterial defense, aimed at producing biotechnological strategies for crop genetic improvement.
The cassava miRNA repertoire is mostly unknown. Up to 20 conserved miRNA families have been indentified in ESTs collections by using bioinformatics approaches [21
] and the expression of 23 mature miRNA families in cassava and other euphorbiaceous has been studied [24
]. However no miRNAs from cassava are currently deposited in miRBase, the consensus database for verified miRNAs [25
]. The first draft of the cassava genome was released in October 2009 and a new version was made available in October 2010 [26
]. This is an important tool for the discovery and prediction of new and specific cassava miRNAs.
This study characterizes the cassava miRNA repertoire using expression data from small RNA libraries and identifies pre-miRNAs in the cassava genome. The miRNA-mediated response to Xam infection in cassava is also analyzed as well as possible transcription factors involved in miRNA regulation.